Finding step aroA for chorismate biosynthesis in Paraburkholderia sp. CCGE1002
No candidates for aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step aroA
- Curated proteins or TIGRFams with EC 2.5.1.19 (search)
- UniProt sequence Q72EV5_DESVH: RecName: Full=3-phosphoshikimate 1-carboxyvinyltransferase {ECO:0000256|HAMAP-Rule:MF_00210}; EC=2.5.1.19 {ECO:0000256|HAMAP-Rule:MF_00210}; AltName: Full=5-enolpyruvylshikimate-3-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_00210}; Short=EPSP synthase {ECO:0000256|HAMAP-Rule:MF_00210}; Short=EPSPS {ECO:0000256|HAMAP-Rule:MF_00210};
- UniProt sequence I9A2E3: RecName: Full=3-phosphoshikimate 1-carboxyvinyltransferase {ECO:0000256|HAMAP-Rule:MF_00210}; EC=2.5.1.19 {ECO:0000256|HAMAP-Rule:MF_00210}; AltName: Full=5-enolpyruvylshikimate-3-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_00210}; Short=EPSP synthase {ECO:0000256|HAMAP-Rule:MF_00210}; Short=EPSPS {ECO:0000256|HAMAP-Rule:MF_00210};
- UniProt sequence L0FR45: RecName: Full=3-phosphoshikimate 1-carboxyvinyltransferase {ECO:0000256|ARBA:ARBA00012450}; EC=2.5.1.19 {ECO:0000256|ARBA:ARBA00012450}; AltName: Full=5-enolpyruvylshikimate-3-phosphate synthase {ECO:0000256|ARBA:ARBA00030046};
- Predicted: UniProt sequence G0EEF0: SubName: Full=EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) {ECO:0000313|EMBL:AEM37991.1};
- Comment: Add AroA from Desulfovibrio vulgaris (DVU0463) because it is a bit diverged, is conserved essential, and clusters with aromatic amino acid biosynthesis genes. HMPREF1058_RS13970 (I9A2E3) is cofit with chorismate synthase (Surya Tripathi); also, it is 71% identical to BT2186 / BT_RS11065, which can complement an aroA- strain of E. coli (Bradley Biggs). PYRFU_RS00635 (G0EEF0) from Pyrolobus fumarii is from this family, has similar active site residues (alignment to Q83E11 shows three conserved residues, and D315 => R331), and its closest homologs are in chorisomate synthesis operons (but, these are under 30% identity); it is probably the missing aroA.
Or cluster all characterized aroA proteins
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory